RetrogeneDB ID: retro_xtro_56

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181419.1:1..1399(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: aldh6a1
• Ensembl ID: ENSXETG00000013304
• Aliases: None
• Description: aldehyde dehydrogenase 6 family, member A1 [Source:Jamboree;Acc:XB-GENE-1006692]

Sequence

>retro_xtro_56
TGGCGCGATGTGACCAATCCCGCCACGCAGGAAGTCGTCGCCCGCGTGCCCTTCGCCACGCGCGACGAGGTGAACCTTGC
CGTCGCCAACGCGCAGCAAGCCTTCCAGACCTGGCGCGAGACGTCGCTGGCCGCGCGCATGCGCATCATGCTGAAGCTGC
AGCAGCTGCTGCGCGAGCACACGGCCGAGTTGGCCCAGCTCATCACGCGCGAGCACGGCAAGACCCTGCCCGACGCCGAG
GGCGAAGTGGCGCGCGGCCTGGAAGTGGTGGAGCACGCCTGCTCCATCACCACGTTGCAGCTCGGCGAGATGGCCGAGAA
TGCCGCCACTGGCGTTGACGTGTACAACCTGCTGCAACCCCTGGGCGTGGGTGCGGGCATCACGGCCTTCAACTTCCCGG
TGATGCTGCCGTGCTTCATGTTTCCCATGGCCATCGCCTGCGGCAATACTTTCGTGCTCAAGCCGTCGGAGCAGGATCCC
AGTTCCACCATGCGTCTGGTGGAACTGGCGCACGAGGCTGGCGTGCCGCCCGGTGTGCTCAATGTGATCCACGGCGGGCC
GGAAGTGGCCGACGTGCTGTGCGACCACCCCGACATCAAGGCGCTGTCATTCATCGGCTCCACCCACGTTGGCACGCACG
TCTACCGCCGCGCCAGCGAGGCGGGCAAGCGCGTGCAGTCGATGATGGGCGCCAAAAACCACTGCGTGGTGATGCCCGAC
GCGCCCAAGGAACACGCGTTGAACAACCTGCTCGGCTCGGCCTTCGGCGCCGCTGGCCAGCGCTGCATGGCCAACTCGGT
GGCGGTGCTCGTGGGCGCGGCGCGCGACTGGCTGCCCGAACTGGTGGAAAAGTCCAAGGCCATGAAGGTTGGCCCCGGCA
GTGACCGCGATGCCGACCTGGGCCCGCTGGTCAACCCGCGCGCCAGGCAGCGCGTGCTGGATCTGATCGACACCGGTGTG
GCCCAAGGCGCCAGACTGCTGCTGGACGGGCGCGGCTGCGTGGTGCCCGGCTATGAAAAGGGCAACTTCGTCGGCCCCAC
GGTGTTCGCCGACGTGACTGAAGCCATGGACATCTACCAGCAGGAGATCTTCGGCCCCGTGCTCAACGTGGTGTGCGTGG
ACACGCTGGAAGACGCCATCGCCTTCATCAACCGCAACCCCAACGGCAACGGCACCTCCATTTTCACCAGCAGCGGCTGG
GCGGCGCGCAGGTTCCAGCACGACATCAACGTCGGCCAGGTGGGCATCAACGTGCCGATCCCCGTGCCCGTGGCCTACTT
CAGCTTCACTGGTTCGCGCGCCTCCAAACTCGGCGACCTGGGCCCCAACGGCAAGCAGGCCGTGCAGTTCTGGACTCAGA
CCAAGACCGTCACCGCCCGCTGGTACGAGGAAGGCAGC

Alignment

ORF - retro_xtro_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.3 %
• Parental protein coverage: 89.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WIDVHNPATNEVIGRVPQATQSEMEAAVNACQRTFPAWSETSILNRQQIFLRYQQLIKDNLKEVARLITL
          W.DV.NPAT.EV..RVP.AT..E...AV...Q..F..W.ETS...R..I.L..QQL......E.A.LIT.
Retrocopy WRDVTNPATQEVVARVPFATRDEVNLAVANAQQAFQTWRETSLAARMRIMLKLQQLLREHTAELAQLITR

Parental  EQGKTLADAEGDVFRGLQVVEHACSVTSLMLGETLSSLTKDMDTFTFRLPLGVCAGIAPFNFPAMIPLWM
          E.GKTL.DAEG.V.RGL.VVEHACS.T.L.LGE.........D......PLGV.AGI..FNFP.M.P..M
Retrocopy EHGKTLPDAEGEVARGLEVVEHACSITTLQLGEMAENAATGVDVYNLLQPLGVGAGITAFNFPVMLPCFM

Parental  FPMAMVCGNTYLMKPSERVPGATMFLVQLLQDAGVPDGTINIIHGQHAAVNFICDHPAIRAISFVGSNQA
          FPMA..CGNT...KPSE..P..TM.LV.L...AGVP.G..N.IHG........CDHP.I.A.SF.GS...
Retrocopy FPMAIACGNTFVLKPSEQDPSSTMRLVELAHEAGVPPGVLNVIHGGPEVADVLCDHPDIKALSFIGSTHV

Parental  GEYIYDRGSRNGKRVQSNMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKQWLPE
          G...Y.R.S..GKRVQS.MGAKNH.VVMPDA.KE..LN.L.G.AFGAAGQRCMA.S.AVLVG.A..WLPE
Retrocopy GTHVYRRASEAGKRVQSMMGAKNHCVVMPDAPKEHALNNLLGSAFGAAGQRCMANSVAVLVGAARDWLPE

Parental  LVEKAKKLQVNAGDQPGADLGPLISPAAKDRVCSLVESGVREGATLLLDGRDVNVKGFENGNFVGPTILA
          LVEK.K...V..G....ADLGPL..P.A..RV..L...GV..GA.LLLDGR...V.G.E.GNFVGPT..A
Retrocopy LVEKSKAMKVGPGSDRDADLGPLVNPRARQRVLDLIDTGVAQGARLLLDGRGCVVPGYEKGNFVGPTVFA

Parental  NVQPHMTCYKEEIFGPVLVILEADTLDDALKIVNSNPYGNGTAIFTTNGATARKYTHLVDVGQVGVNVPI
          .V...M..Y..EIFGPVL.....DTL.DA....N.NP.GNGT.IFT..G..AR...H...VGQVG.NVPI
Retrocopy DVTEAMDIYQQEIFGPVLNVVCVDTLEDAIAFINRNPNGNGTSIFTSSGWAARRFQHDINVGQVGINVPI

Parental  PVPLPMFSFTGSRASFRGDTNFYGKQGVHFYTQLKTVTSQWKEEDS
          PVP...FSFTGSRAS..GD....GKQ.V.F.TQ.KTVT..W.EE.S
Retrocopy PVPVAYFSFTGSRASKLGDLGPNGKQAVQFWTQTKTVTARWYEEGS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	46.87 RPM
SRP007412_heart	0.00 RPM	162.80 RPM
SRP007412_kidney	0.00 RPM	162.80 RPM
SRP007412_liver	0.00 RPM	91.67 RPM
SRP007412_skeletal_muscle	0.00 RPM	63.56 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_56 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_56 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002670	1 retrocopy	retro_chof_2670,
Xenopus tropicalis	ENSXETG00000013304	1 retrocopy	retro_xtro_56 ,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,